Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007985.1 Hibiscus syriacus cultivar Beakdansim tig00110430_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2235968
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:325402 original size:2 final size:2
Alignment explanation
Indices: 325395--325456 Score: 90
Period size: 2 Copynumber: 31.0 Consensus size: 2
325385 TTATTTTCTC
*
325395 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT GAT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
*
325438 AT A- AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
325457 GTTTATTTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
1 1 0.02
2 52 0.96
3 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:329770 original size:31 final size:31
Alignment explanation
Indices: 329732--329984 Score: 470
Period size: 31 Copynumber: 8.2 Consensus size: 31
329722 GGTCACAATA
329732 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
329763 TAGACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
329794 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
329825 TAGACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
329856 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
329887 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
329918 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
329949 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
329980 TAAAC
1 TAAAC
329985 CCTCGACTCT
Statistics
Matches: 214, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 214 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:330628 original size:64 final size:64
Alignment explanation
Indices: 330542--330703 Score: 213
Period size: 64 Copynumber: 2.5 Consensus size: 64
330532 TATTATTGCT
* *
330542 GGATGCATCGATGCACTCCTTATGCATCGATGCATCG-ATTGCATTCGATGT-TTCACTATTAAT
1 GGATGCATCGATGCACTACTTATGCATCGATGCA-CGAATTGCATTCGATGTCTTCA-TATTAAA
330605 G
64 G
* *
330606 GGATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTATTTTAAAG
1 GGATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTCATATTAAAG
* ** *
330670 AG-TGCATCGATGCACTACCAATGCATCGGTGCAC
1 GGATGCATCGATGCACTACTTATGCATCGATGCAC
330704 ATTCAAAAAT
Statistics
Matches: 88, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
63 31 0.35
64 54 0.61
65 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (64 bp):
GGATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTCATATTAAAG
Found at i:332017 original size:42 final size:42
Alignment explanation
Indices: 331959--332044 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
331949 CGTGGCAAGT
*
331959 AGAGTTAATGACGTTGTCGTGGTAAGTGAAGTTGCCAAGGCA
1 AGAGTTAATGACGTTGTCGTGGCAAGTGAAGTTGCCAAGGCA
* * *
332001 AGAGTTAATGATGTTGTCGTGGCAAGTGACGTTGCCATGGCA
1 AGAGTTAATGACGTTGTCGTGGCAAGTGAAGTTGCCAAGGCA
332043 AG
1 AG
332045 TATAGGATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.27, C:0.13, G:0.34, T:0.27
Consensus pattern (42 bp):
AGAGTTAATGACGTTGTCGTGGCAAGTGAAGTTGCCAAGGCA
Found at i:341445 original size:2 final size:2
Alignment explanation
Indices: 341438--341469 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
341428 CGATCAGATG
341438 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
341470 GTATGTGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:342906 original size:22 final size:22
Alignment explanation
Indices: 342878--342923 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
342868 TTACCTTAAC
342878 ATCATATATTTTTCAGACGACT
1 ATCATATATTTTTCAGACGACT
342900 ATCATATATTTTTCAGACGACT
1 ATCATATATTTTTCAGACGACT
342922 AT
1 AT
342924 AGTTTCTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (22 bp):
ATCATATATTTTTCAGACGACT
Found at i:344206 original size:29 final size:29
Alignment explanation
Indices: 344173--344228 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
344163 TACCAACACA
* * *
344173 TAGGTCGTCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGAGACCTTG
344202 TAGGTCGCCATGCACTCCGGGAGACCT
1 TAGGTCGCCATGCACTCCGGGAGACCT
344229 ACCCTTGCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.14, C:0.34, G:0.30, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGAGACCTTG
Found at i:344293 original size:23 final size:23
Alignment explanation
Indices: 344239--344294 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
344229 ACCCTTGCTC
* * *
344239 GCTCGCTCAGCTGCCCTCGCATT
1 GCTCGCTCGGCTGCCCTCGAATA
344262 GCTCGCTCGGCTGCCCTCGAATA
1 GCTCGCTCGGCTGCCCTCGAATA
344285 GCTCGCTCGG
1 GCTCGCTCGG
344295 ATAACCTCGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.09, C:0.41, G:0.27, T:0.23
Consensus pattern (23 bp):
GCTCGCTCGGCTGCCCTCGAATA
Found at i:344302 original size:23 final size:23
Alignment explanation
Indices: 344253--344303 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
344243 GCTCAGCTGC
* * * **
344253 CCTCGCATTGCTCGCTCGGCTGC
1 CCTCGAATAGCTCGCTCGGATAA
344276 CCTCGAATAGCTCGCTCGGATAA
1 CCTCGAATAGCTCGCTCGGATAA
344299 CCTCG
1 CCTCG
344304 GATGCTCTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.14, C:0.39, G:0.24, T:0.24
Consensus pattern (23 bp):
CCTCGAATAGCTCGCTCGGATAA
Found at i:345633 original size:2 final size:2
Alignment explanation
Indices: 345628--345669 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
345618 ACACGCACAC
345628 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
345670 TGATGTGATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:346346 original size:28 final size:31
Alignment explanation
Indices: 346297--346362 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 31
346287 ATCTAACGAC
*
346297 CTATAATTGAAACGAAAATT-AAAGTTCAATA
1 CTATAATT-AAACGAAAATTAAAAGTCCAATA
346328 CTATAATT-AAC-AAAATTAAAAGTCCAATA
1 CTATAATTAAACGAAAATTAAAAGTCCAATA
*
346357 ATATAA
1 CTATAA
346363 ATGATACGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 6 0.19
29 18 0.56
31 8 0.25
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.29
Consensus pattern (31 bp):
CTATAATTAAACGAAAATTAAAAGTCCAATA
Found at i:353924 original size:24 final size:24
Alignment explanation
Indices: 353892--353940 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
353882 TGTATGACGC
353892 TGAAACATTGCTCATAAGTCATGT
1 TGAAACATTGCTCATAAGTCATGT
*
353916 TGAAACATTGCTCATAAGTCTTGT
1 TGAAACATTGCTCATAAGTCATGT
353940 T
1 T
353941 TCAGCTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (24 bp):
TGAAACATTGCTCATAAGTCATGT
Found at i:354831 original size:23 final size:22
Alignment explanation
Indices: 354779--354852 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 22
354769 CAGCTTGTAT
354779 AAATGCACCGAAGTGCCACGTA-
1 AAATGCA-CGAAGTGCCACGTAG
* *
354801 AGATTGCATCGAAGTGCCGCGTAG
1 A-AATGCA-CGAAGTGCCACGTAG
*
354825 AAATGCACTGAAGTGGCACGTAG
1 AAATGCAC-GAAGTGCCACGTAG
354848 AAATG
1 AAATG
354853 TCCATAAGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
22 2 0.05
23 40 0.93
24 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.18
Consensus pattern (22 bp):
AAATGCACGAAGTGCCACGTAG
Found at i:357746 original size:23 final size:23
Alignment explanation
Indices: 357709--357772 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
357699 AAACTTGTAT
357709 AAATGCACC-TAAGTGCCACGTAG
1 AAATGCACCGT-AGTGCCACGTAG
* *
357732 AATTGCACCGTAGTGCCGCGTAG
1 AAATGCACCGTAGTGCCACGTAG
*
357755 AAATGCACCGAAGTGCCA
1 AAATGCACCGTAGTGCCA
357773 TATAATAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (23 bp):
AAATGCACCGTAGTGCCACGTAG
Found at i:357880 original size:2 final size:2
Alignment explanation
Indices: 357875--357906 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
357865 GTTCCAAAGA
357875 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
357907 CCCGAAGGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:359236 original size:21 final size:21
Alignment explanation
Indices: 359212--359256 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
359202 TTTTGTTCGT
* *
359212 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
359233 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
359254 TTG
1 TTG
359257 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:362112 original size:12 final size:12
Alignment explanation
Indices: 362095--362125 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
362085 AGTTCGAGAG
362095 TTCCCTGATGTT
1 TTCCCTGATGTT
*
362107 TTCCCTGTTGTT
1 TTCCCTGATGTT
362119 TTCCCTG
1 TTCCCTG
362126 CTGAGTTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.03, C:0.29, G:0.16, T:0.52
Consensus pattern (12 bp):
TTCCCTGATGTT
Found at i:366562 original size:23 final size:23
Alignment explanation
Indices: 366536--366588 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
366526 TATGGCATTA
366536 CGGTGCAATTCTACGCGGCACTT
1 CGGTGCAATTCTACGCGGCACTT
*
366559 CGGTGCAATTCTATGCGGCACTT
1 CGGTGCAATTCTACGCGGCACTT
366582 CGGTGCA
1 CGGTGCA
366589 TTTATACGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.26
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTT
Found at i:367753 original size:17 final size:18
Alignment explanation
Indices: 367721--367759 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
367711 ATCTAATATT
367721 ATTTATTTACTAAG-TTA
1 ATTTATTTACTAAGTTTA
* *
367738 ATTTATTTATTTAGTTTA
1 ATTTATTTACTAAGTTTA
367756 ATTT
1 ATTT
367760 CACATGACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (18 bp):
ATTTATTTACTAAGTTTA
Found at i:368934 original size:18 final size:17
Alignment explanation
Indices: 368901--368934 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
368891 CATTCAAAAA
*
368901 CTCTTAATCTTTAATCT
1 CTCTTAATCCTTAATCT
368918 CTCTTAACTCCTTAATC
1 CTCTTAA-TCCTTAATC
368935 CCTTGATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (17 bp):
CTCTTAATCCTTAATCT
Found at i:370017 original size:7 final size:7
Alignment explanation
Indices: 370005--370036 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
369995 CTGAATTTCC
370005 AACAGTA
1 AACAGTA
370012 AACAGTA
1 AACAGTA
*
370019 AACTGTA
1 AACAGTA
370026 AACAGTA
1 AACAGTA
370033 AACA
1 AACA
370037 ACATTTGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (7 bp):
AACAGTA
Found at i:375497 original size:23 final size:23
Alignment explanation
Indices: 375463--375531 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
375453 CACCACAGCT
*
375463 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
375486 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
375509 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
375532 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:375541 original size:23 final size:23
Alignment explanation
Indices: 375469--375541 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
375459 AGCTCGTATA
*
375469 AATGCACCGAAGTGCCACGTAGAAT
1 AATGCACCGAAGTGCCA--TATAAT
* *
375494 --TGCACCGTAGTGCCGCGTAT-A-
1 AATGCACCGAAGTG-C-CATATAAT
375515 AATGCACCGAAGTGCCATATAAT
1 AATGCACCGAAGTGCCATATAAT
375538 AATG
1 AATG
375542 TCCATAAGGA
Statistics
Matches: 37, Mismatches: 5, Indels: 14
0.66 0.09 0.25
Matches are distributed among these distances:
21 4 0.11
22 3 0.08
23 28 0.76
24 1 0.03
25 1 0.03
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (23 bp):
AATGCACCGAAGTGCCATATAAT
Found at i:376979 original size:21 final size:21
Alignment explanation
Indices: 376955--376999 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
376945 TTTTGTTCGT
*
376955 TTGAAAGGGTATCGGTTCCCC
1 TTGAAAGGGTATCGATTCCCC
*
376976 TTGAATGGGTATCGATTCCCC
1 TTGAAAGGGTATCGATTCCCC
376997 TTG
1 TTG
377000 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (21 bp):
TTGAAAGGGTATCGATTCCCC
Found at i:377923 original size:16 final size:16
Alignment explanation
Indices: 377884--377926 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
377874 ATCATCGGTT
*
377884 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
377900 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
377917 CTTATCAATC
1 CTTATCAATC
377927 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:382075 original size:21 final size:21
Alignment explanation
Indices: 382051--382095 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
382041 TTTTGTTCGT
*
382051 TTGAAGGGGTA-TCGGTTCCCC
1 TTGAAGGGGTACT-GATTCCCC
*
382072 TTGAATGGGTACTGATTCCCC
1 TTGAAGGGGTACTGATTCCCC
382093 TTG
1 TTG
382096 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACTGATTCCCC
Found at i:382948 original size:29 final size:30
Alignment explanation
Indices: 382904--382968 Score: 105
Period size: 29 Copynumber: 2.2 Consensus size: 30
382894 TCTATGTTTT
* *
382904 TGATGATATGATATTATTACGTGTCTAAAG
1 TGATGATATGACATTATTACGTGTCTAAAA
382934 TGATGA-ATGACATTATTACGTGTCTAAAA
1 TGATGATATGACATTATTACGTGTCTAAAA
382963 TGATGA
1 TGATGA
382969 CGTAACATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
29 27 0.82
30 6 0.18
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (30 bp):
TGATGATATGACATTATTACGTGTCTAAAA
Found at i:387341 original size:2 final size:2
Alignment explanation
Indices: 387334--387379 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
387324 GTAGCGGCAG
387334 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
387376 GA GA
1 GA GA
387380 AGTTGGTATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:390610 original size:17 final size:18
Alignment explanation
Indices: 390578--390612 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
390568 TATTTATGAA
390578 ATTTTAAAATTATTTTAT
1 ATTTTAAAATTATTTTAT
*
390596 ATTTT-AAATTTTTTTAT
1 ATTTTAAAATTATTTTAT
390613 GTATATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTAAAATTATTTTAT
Found at i:390636 original size:23 final size:21
Alignment explanation
Indices: 390610--390654 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
390600 TAAATTTTTT
390610 TATGTATAT-ATTTTTATTGAAAA
1 TATGT-TATCATTTTT-TT-AAAA
390633 TATGTTATCATTTTTTTAAAA
1 TATGTTATCATTTTTTTAAAA
390654 T
1 T
390655 TTTACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 5 0.24
22 5 0.24
23 11 0.52
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (21 bp):
TATGTTATCATTTTTTTAAAA
Found at i:392507 original size:90 final size:91
Alignment explanation
Indices: 392329--392509 Score: 346
Period size: 90 Copynumber: 2.0 Consensus size: 91
392319 ACCACATGCT
*
392329 CATATACCACTATAGAATACTTATGTAACTTCAATTTTATTTGTTTTTACTAAAAATGTACTCTC
1 CATATACCACTATAGAATACTTATATAACTTCAATTTTATTTGTTTTTACTAAAAATGTACTCTC
392394 TTTTTTATTTATACCCTTAACATTGC
66 TTTTTTATTTATACCCTTAACATTGC
392420 CATATACCACTATAGAATACTTATATAACTTCAATTTTATTT-TTTTTACTAAAAATGTACTCTC
1 CATATACCACTATAGAATACTTATATAACTTCAATTTTATTTGTTTTTACTAAAAATGTACTCTC
392484 TTTTTTATTTATACCCTTAACATTGC
66 TTTTTTATTTATACCCTTAACATTGC
392510 ATTTTACTCA
Statistics
Matches: 89, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
90 48 0.54
91 41 0.46
ACGTcount: A:0.31, C:0.18, G:0.04, T:0.46
Consensus pattern (91 bp):
CATATACCACTATAGAATACTTATATAACTTCAATTTTATTTGTTTTTACTAAAAATGTACTCTC
TTTTTTATTTATACCCTTAACATTGC
Found at i:393207 original size:83 final size:82
Alignment explanation
Indices: 393091--393319 Score: 225
Period size: 82 Copynumber: 2.8 Consensus size: 82
393081 CTTTAGCGGT
* * * *
393091 GTTTTCCCAACAAAC-ACCGAAATAGAGTGGTAATTTAGCGGCGTTTATAGCT-AAAACGCCGGA
1 GTTTTTCCAACAAACGA-CGCAATAGAGTAGTAATTTAGCGGCGTTTATA--TAAAAACGCCGCA
*
393154 A-TTGAATTGTTTACAGTGGC
63 ACATG-ATTGTTTACAGTGGC
* * * * * *
393174 GTTTTTTCAATAAACG-CTGCAATAGAGTAGTAATTTCGTGGCGTTTGTATAAAAATGCCGCAAC
1 GTTTTTCCAACAAACGAC-GCAATAGAGTAGTAATTTAGCGGCGTTTATATAAAAACGCCGCAAC
*
393238 ATGATTGTTTATAGTGGC
65 ATGATTGTTTACAGTGGC
* * *
393256 GTTTTTCCAACAAACGACGCTATAGAGAATTAATTTAGCGGCGTTTATCA-AACAAACGCCGCAA
1 GTTTTTCCAACAAACGACGCAATAGAGTAGTAATTTAGCGGCGTTTAT-ATAA-AAACGCCGCAA
393320 TAGATTTGTT
Statistics
Matches: 118, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
81 1 0.01
82 65 0.55
83 52 0.44
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (82 bp):
GTTTTTCCAACAAACGACGCAATAGAGTAGTAATTTAGCGGCGTTTATATAAAAACGCCGCAACA
TGATTGTTTACAGTGGC
Found at i:394635 original size:43 final size:43
Alignment explanation
Indices: 394541--394710 Score: 157
Period size: 43 Copynumber: 4.0 Consensus size: 43
394531 CATATAGCGG
* * * *
394541 CAACAAACGCCGCAAAAGGTATTGATATTTAGCGGC-ATTTTT
1 CAACAAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTTTT
* ** *
394583 CAGAAAAACGCCGCAATAGGCGTTGATGTTTAGCGGCGTTTTCTT
1 CA-ACAAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTT-TT
* * * * * *
394628 C-ACAAACGCCGCAGTAGATGTTTATTTTTACCGACGTTTTTC
1 CAACAAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTTTT
*
394670 CTACAAACGCCGCAGA-AGATGTTGATATTTAGCGGCGTTTT
1 CAACAAACGCCGCA-ATAGATGTTGATATTTAGCGGCGTTTT
394711 CCTACAAACA
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
42 4 0.04
43 93 0.90
44 3 0.03
45 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (43 bp):
CAACAAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTTTT
Found at i:396279 original size:41 final size:41
Alignment explanation
Indices: 396234--396424 Score: 151
Period size: 40 Copynumber: 4.7 Consensus size: 41
396224 TTAAAATCAA
*
396234 TTGCGGCGTTTAC-AGAAAAACGCCACTAATGTACGACCCAT
1 TTGCGGCGTTT-CTAGAAAAACGCCACTAATGTACAACCCAT
* * * * *
396275 TTGCGGCGTTTCTTGTAAAACGACACT-AT-AAGCAACTC-T
1 TTGCGGCGTTTCTAGAAAAACGCCACTAATGTA-CAACCCAT
* *
396314 ATTGCGGCGTTTATATAAAAACGCCACTAATGTACAACCCAT
1 -TTGCGGCGTTTCTAGAAAAACGCCACTAATGTACAACCCAT
* * * ** *
396356 TTGCAGCGTTTCTTGTAAAACGCCACT-ATAAACAACTC-T
1 TTGCGGCGTTTCTAGAAAAACGCCACTAATGTACAACCCAT
* * *
396395 ATTGCGGCGTTTATATAAAAACGCCGCTAA
1 -TTGCGGCGTTTCTAGAAAAACGCCACTAA
396425 ATTACTACTC
Statistics
Matches: 115, Mismatches: 27, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
39 3 0.03
40 58 0.50
41 52 0.45
42 2 0.02
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (41 bp):
TTGCGGCGTTTCTAGAAAAACGCCACTAATGTACAACCCAT
Found at i:396325 original size:81 final size:81
Alignment explanation
Indices: 396233--396499 Score: 378
Period size: 81 Copynumber: 3.3 Consensus size: 81
396223 GTTAAAATCA
* * *
396233 ATTGCGGCGTTTACAGAAAAACGCCACTAATGTACGACCCATTTGCGGCGTTTCTTGTAAAACGA
1 ATTGCGGCGTTTATATAAAAACGCCACTAATGTACAACCCATTTGCGGCGTTTCTTGTAAAACGA
*
396298 CACTATAAGCAACTCT
66 CACTATAAACAACTCT
* *
396314 ATTGCGGCGTTTATATAAAAACGCCACTAATGTACAACCCATTTGCAGCGTTTCTTGTAAAACGC
1 ATTGCGGCGTTTATATAAAAACGCCACTAATGTACAACCCATTTGCGGCGTTTCTTGTAAAACGA
396379 CACTATAAACAACTCT
66 CACTATAAACAACTCT
* * * * *
396395 ATTGCGGCGTTTATATAAAAACGCCGCTAAAT-TACTACTC-TATTGCGGTGTTTTTTAG-AAAA
1 ATTGCGGCGTTTATATAAAAACGCCACT-AATGTACAACCCAT-TTGCGGCGTTTCTT-GTAAAA
*
396457 CGTCACTATAAACAACTCT
63 CGACACTATAAACAACTCT
396476 ATTGCGGCGTTTATATAAAAACGC
1 ATTGCGGCGTTTATATAAAAACGC
396500 AGCTAAATTA
Statistics
Matches: 170, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
80 1 0.01
81 165 0.97
82 4 0.02
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (81 bp):
ATTGCGGCGTTTATATAAAAACGCCACTAATGTACAACCCATTTGCGGCGTTTCTTGTAAAACGA
CACTATAAACAACTCT
Found at i:396457 original size:41 final size:41
Alignment explanation
Indices: 396307--396548 Score: 223
Period size: 41 Copynumber: 5.9 Consensus size: 41
396297 ACACTATAAG
*
396307 CAACTCTATTGCGGCGTTTATATAAAAACGCCACT-AATGTA
1 CAACTCTATTGCGGCGTTTATATAAAAACGCCGCTAAAT-TA
* * * * *
396348 CAAC-CCATTTGCAGCGTTTCT-TGTAAAACGCCACTATAA--A
1 CAACTCTA-TTGCGGCGTTTATAT-AAAAACGCCGCTA-AATTA
396388 CAACTCTATTGCGGCGTTTATATAAAAACGCCGCTAAATTA
1 CAACTCTATTGCGGCGTTTATATAAAAACGCCGCTAAATTA
* * * * *
396429 CTACTCTATTGCGGTGTTT-TTTAGAAAACGTCACTATAA--A
1 CAACTCTATTGCGGCGTTTATATA-AAAACGCCGCTA-AATTA
*
396469 CAACTCTATTGCGGCGTTTATATAAAAACGCAGCTAAATTA
1 CAACTCTATTGCGGCGTTTATATAAAAACGCCGCTAAATTA
* *
396510 CCACTCTATTGCGGCGTTTGT-TGAAAAAACGCCGCTAAA
1 CAACTCTATTGCGGCGTTTATAT--AAAAACGCCGCTAAA
396549 GTTTCATTTT
Statistics
Matches: 163, Mismatches: 23, Indels: 29
0.76 0.11 0.13
Matches are distributed among these distances:
39 4 0.02
40 61 0.37
41 80 0.49
42 16 0.10
43 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (41 bp):
CAACTCTATTGCGGCGTTTATATAAAAACGCCGCTAAATTA
Found at i:396507 original size:81 final size:80
Alignment explanation
Indices: 396233--396536 Score: 350
Period size: 81 Copynumber: 3.8 Consensus size: 80
396223 GTTAAAATCA
* * * *
396233 ATTGCGGCGTTTACAGAAAAACGCCA-CT-AATGTACGAC-CCATTTGCGGCGTTTCTTGTAAAA
1 ATTGCGGCGTTTATATAAAAACG-CAGCTAAAT-TACAACTCTA-TTGCGGCGTTTCTTG-AAAA
*
396295 CGACACTATAAGCAACTCT
62 CGACACTATAAACAACTCT
* *
396314 ATTGCGGCGTTTATATAAAAACGCCA-CT-AATGTACAAC-CCATTTGCAGCGTTTCTTGTAAAA
1 ATTGCGGCGTTTATATAAAAACG-CAGCTAAAT-TACAACTCTA-TTGCGGCGTTTCTTG-AAAA
*
396376 CGCCACTATAAACAACTCT
62 CGACACTATAAACAACTCT
* * * * *
396395 ATTGCGGCGTTTATATAAAAACGCCGCTAAATTACTACTCTATTGCGGTGTTTTTTAGAAAACGT
1 ATTGCGGCGTTTATATAAAAACGCAGCTAAATTACAACTCTATTGCGGCGTTTCTT-GAAAACGA
396460 CACTATAAACAACTCT
65 CACTATAAACAACTCT
* *
396476 ATTGCGGCGTTTATATAAAAACGCAGCTAAATTACCACTCTATTGCGGCGTTTGTTGAAAA
1 ATTGCGGCGTTTATATAAAAACGCAGCTAAATTACAACTCTATTGCGGCGTTTCTTGAAAA
396537 AACGCCGCTA
Statistics
Matches: 202, Mismatches: 17, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
80 6 0.03
81 190 0.94
82 6 0.03
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (80 bp):
ATTGCGGCGTTTATATAAAAACGCAGCTAAATTACAACTCTATTGCGGCGTTTCTTGAAAACGAC
ACTATAAACAACTCT
Found at i:398487 original size:24 final size:24
Alignment explanation
Indices: 398424--398524 Score: 148
Period size: 24 Copynumber: 4.0 Consensus size: 24
398414 CTTAGGACGC
*
398424 ATGAAGTGTTGTTTTTAAGAGACAAATA
1 ATGAAGTATTG-TTTTAAGAGAC--A-A
*
398452 ATGAAGTGTTGTTTTAAGAGACAA
1 ATGAAGTATTGTTTTAAGAGACAA
398476 ATGAAGTATTGTTTTAAGAGACAA
1 ATGAAGTATTGTTTTAAGAGACAA
398500 ATGAAGTATTGTTTTAAGAGACAA
1 ATGAAGTATTGTTTTAAGAGACAA
398524 A
1 A
398525 CTTATTATGA
Statistics
Matches: 72, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
24 49 0.68
25 1 0.01
27 11 0.15
28 11 0.15
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.34
Consensus pattern (24 bp):
ATGAAGTATTGTTTTAAGAGACAA
Found at i:398695 original size:18 final size:18
Alignment explanation
Indices: 398672--398706 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
398662 TAGCAAATAA
*
398672 ATGTGAACTTAAATTATT
1 ATGTGAAATTAAATTATT
398690 ATGTGAAATTAAATTAT
1 ATGTGAAATTAAATTAT
398707 GTGTGTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (18 bp):
ATGTGAAATTAAATTATT
Found at i:404254 original size:21 final size:21
Alignment explanation
Indices: 404222--404355 Score: 85
Period size: 21 Copynumber: 6.4 Consensus size: 21
404212 AGCGGAAAAT
404222 GAAGCAAG-GGAAGCAGAGAGA
1 GAAGC-AGCGGAAGCAGAGAGA
* * **
404243 GCAGCAGCGGAAGTAGCCAGA
1 GAAGCAGCGGAAGCAGAGAGA
* * * *
404264 GCAGTAGCAGAAGCAGAGAAA
1 GAAGCAGCGGAAGCAGAGAGA
*
404285 GAAGCAGC-GACAGCATAGAGA
1 GAAGCAGCGGA-AGCAGAGAGA
* * * *
404306 GATGCAGCAGCAGCACAGAGA
1 GAAGCAGCGGAAGCAGAGAGA
* *
404327 GAAGC-GACGGTAGCACAGAGA
1 GAAGCAG-CGGAAGCAGAGAGA
404348 GAAGCAGC
1 GAAGCAGC
404356 ATATCAGTAG
Statistics
Matches: 88, Mismatches: 20, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
20 5 0.06
21 81 0.92
22 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.37, T:0.04
Consensus pattern (21 bp):
GAAGCAGCGGAAGCAGAGAGA
Found at i:404776 original size:43 final size:43
Alignment explanation
Indices: 404715--404980 Score: 157
Period size: 43 Copynumber: 6.2 Consensus size: 43
404705 CCTAACTTTA
* * *
404715 GCGGCGTTTGT-ATGAAAACGCCACTAAATCTCAACACCTATT
1 GCGGCATTTGTAATAAAAACGCCGCTAAATCTCAACACCTATT
* * * *
404757 GCGGCATTT-TCAATAAAAACACCGCTAATTCTCAACTCTTATT
1 GCGGCATTTGT-AATAAAAACGCCGCTAAATCTCAACACCTATT
* * * * * * *
404800 GCGTCATTT-TCGATACAAACTCCGCTAAATCTGAA-AGTCTACT
1 GCGGCATTTGT-AATAAAAACGCCGCTAAATCTCAACA-CCTATT
* * *** * * * * *
404843 GCGACGTTTGTGGGAAAAAGGCCACAAAATATCAAAACCT-TCT
1 GCGGCATTTGTAATAAAAACGCCGCTAAATCTCAACACCTAT-T
* *
404886 GCGGCGTTTGTAAGT-AAAACGCCGCTAAATCTCAAAACCTATT
1 GCGGCATTTGTAA-TAAAAACGCCGCTAAATCTCAACACCTATT
* * *** *
404929 GCGACGTTTGTAGGGAAAACGCCGCTAAATATCAACACCTATT
1 GCGGCATTTGTAATAAAAACGCCGCTAAATCTCAACACCTATT
404972 GCGGCATTT
1 GCGGCATTT
404981 TTCTGACAAA
Statistics
Matches: 170, Mismatches: 45, Indels: 17
0.73 0.19 0.07
Matches are distributed among these distances:
41 1 0.01
42 8 0.05
43 158 0.93
44 3 0.02
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (43 bp):
GCGGCATTTGTAATAAAAACGCCGCTAAATCTCAACACCTATT
Found at i:404975 original size:86 final size:86
Alignment explanation
Indices: 404715--404976 Score: 212
Period size: 86 Copynumber: 3.1 Consensus size: 86
404705 CCTAACTTTA
* * * * * *** *
404715 GCGGCGTTTGTATG-AAAACGCCACTAAATCTCAACACCTATTGCGGCATTT-TCAATAAAAACA
1 GCGGCGTTTGTAAGTAAAACGCCGCTAAATCTCAAAACCTATTGCGACGTTTGT-AGGGAAAACG
* * * *
404778 CCGCTAATTCTCAACTCTTATT
65 CCGCTAAATATCAACACCTATT
* * * * * ** *
404800 GCGTCATTT-T-CGATACAAACTCCGCTAAATCTGAAAGTCTACTGCGACGTTTGT-GGGAAAAA
1 GCGGCGTTTGTAAG-TA-AAACGCCGCTAAATCTCAAAACCTATTGCGACGTTTGTAGGG-AAAA
* * * *
404862 GGCCACAAAATATCAAAACCT-TCT
63 CGCCGCTAAATATCAACACCTAT-T
404886 GCGGCGTTTGTAAGTAAAACGCCGCTAAATCTCAAAACCTATTGCGACGTTTGTAGGGAAAACGC
1 GCGGCGTTTGTAAGTAAAACGCCGCTAAATCTCAAAACCTATTGCGACGTTTGTAGGGAAAACGC
404951 CGCTAAATATCAACACCTATT
66 CGCTAAATATCAACACCTATT
404972 GCGGC
1 GCGGC
404977 ATTTTTCTGA
Statistics
Matches: 131, Mismatches: 36, Indels: 19
0.70 0.19 0.10
Matches are distributed among these distances:
83 1 0.01
84 1 0.01
85 9 0.07
86 111 0.85
87 8 0.06
88 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (86 bp):
GCGGCGTTTGTAAGTAAAACGCCGCTAAATCTCAAAACCTATTGCGACGTTTGTAGGGAAAACGC
CGCTAAATATCAACACCTATT
Found at i:407679 original size:2 final size:2
Alignment explanation
Indices: 407639--407663 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
407629 ATCCGGCCCA
407639 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
407664 ATTTTATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:412370 original size:27 final size:27
Alignment explanation
Indices: 412340--412393 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
412330 CACCAACGAG
412340 AATATTTTATACATCACCAAACTCTTT
1 AATATTTTATACATCACCAAACTCTTT
*
412367 AATATTTTTTACATCACCAAACTCTTT
1 AATATTTTATACATCACCAAACTCTTT
412394 CTTACATGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (27 bp):
AATATTTTATACATCACCAAACTCTTT
Found at i:418044 original size:12 final size:13
Alignment explanation
Indices: 418019--418047 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
418009 ATGGCTAATT
418019 GTCCTAGTTCCTA
1 GTCCTAGTTCCTA
418032 GTCCTAG-TCCTA
1 GTCCTAGTTCCTA
418044 GTCC
1 GTCC
418048 CATAGCTGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.14, C:0.34, G:0.17, T:0.34
Consensus pattern (13 bp):
GTCCTAGTTCCTA
Found at i:418186 original size:3 final size:3
Alignment explanation
Indices: 418178--418215 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
418168 TGCTTTTTGT
418178 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
418216 CACAGAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:419662 original size:22 final size:22
Alignment explanation
Indices: 419630--419671 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
419620 TATAAAAAAT
419630 TATTTGTTATTAAATATTTTTTG
1 TATTTGTTATTAAAT-TTTTTTG
*
419653 TATTT-TTATTTAATTTTTT
1 TATTTGTTATTAAATTTTTT
419672 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 8 0.44
23 5 0.28
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (22 bp):
TATTTGTTATTAAATTTTTTTG
Found at i:422146 original size:4 final size:4
Alignment explanation
Indices: 422139--422308 Score: 340
Period size: 4 Copynumber: 42.5 Consensus size: 4
422129 AATATATATA
422139 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
422187 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
422235 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
422283 TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TA
422309 CATCTGATTC
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 166 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:427740 original size:16 final size:17
Alignment explanation
Indices: 427719--427763 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
427709 AACATTCTCA
427719 GTAATCTTATTCC-CTG
1 GTAATCTTATTCCACTG
427735 GTAATCTTACATTCCTACTG
1 GTAATCTT--ATTCC-ACTG
427755 GTAATCTTA
1 GTAATCTTA
427764 CATTCTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 6 0.24
20 11 0.44
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.42
Consensus pattern (17 bp):
GTAATCTTATTCCACTG
Found at i:432649 original size:2 final size:2
Alignment explanation
Indices: 432642--432696 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
432632 TTTACTAATT
432642 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
432684 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
432697 TTATTTATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:432781 original size:2 final size:2
Alignment explanation
Indices: 432774--432812 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
432764 CTATACTTTA
432774 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
432813 CTGTTAATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:438514 original size:68 final size:67
Alignment explanation
Indices: 438404--438535 Score: 171
Period size: 68 Copynumber: 2.0 Consensus size: 67
438394 AGAAATACTT
* * *
438404 CGTTTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAAAAGGAAAAA-A-GAAAAAAGAG
1 CGTTTAGGATGAAAACCCGAAAGGGCGCCCTAAATTG--AAAAAA-GAAAAAGAGGAAAAAAGAG
438467 AAGAA
63 AAGAA
*
438472 CGTTTAGGGTGAAAACCCGAAAGGGCGCCCTAAATT-AGAAAAAGAAAAAGAGGAAAAAAGAGAA
1 CGTTTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGA-AAAAAGAAAAAGAGGAAAAAAGAGAA
438536 CAAAAGAAGA
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
65 7 0.12
66 6 0.11
67 12 0.21
68 32 0.56
ACGTcount: A:0.51, C:0.11, G:0.27, T:0.11
Consensus pattern (67 bp):
CGTTTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAAAAAAGAAAAAGAGGAAAAAAGAGAAG
AA
Found at i:439477 original size:105 final size:105
Alignment explanation
Indices: 439295--440068 Score: 1239
Period size: 105 Copynumber: 7.4 Consensus size: 105
439285 AGGTCTTACC
* * *
439295 CAGAGTCAATTTCAACTTCACAACGAATGATATTGAACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
439360 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * * *
439400 CAGAGCCAATTTCCACTTCACGACAAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
439465 ACGAAGGGACCGCTAGTTGTCAATAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
439505 CAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
439570 ACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
439610 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
439675 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
439715 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
439780 ACGAAGGGACCGCTGGTTGTCCATAAACA--TCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
439818 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTACAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
439883 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * *
439923 CAGAGCCAATTTCAACTCCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
** * *
439988 ACGAAGGGATGGCTGGTTGTCAACAAACAATTTC-CCAGTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * * *
440028 CTAGAACCAATTTCAACTCCACGACGGAGGATATTGGACTC
1 C-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
440069 GGAACAATAC
Statistics
Matches: 622, Mismatches: 43, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
103 98 0.16
105 483 0.78
106 41 0.07
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:439966 original size:313 final size:314
Alignment explanation
Indices: 439295--440068 Score: 1273
Period size: 313 Copynumber: 2.5 Consensus size: 314
439285 AGGTCTTACC
* * *
439295 CAGAGTCAATTTCAACTTCACAACGAATGATATTGAACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
439360 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCCACTTCACGACA
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGAGCCAATTTCAACTTCACGACG
439425 AAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAATA
131 AAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAATA
* *
439490 AACATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGC
196 AACA-TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACGC
439555 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATTT
260 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATTT
*
439610 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
439675 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGAGCCAATTTCAACTTCACGACG
* * *
439740 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCCATA
131 AAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAATA
* *
439805 AACA-TCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTACAGACAACGCA
196 AACATTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACGCA
*
439869 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
261 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATTT
* * *
439923 CAGAGCCAATTTCAACTCCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
** * * *
439988 ACGAAGGGATGGCTGGTTGTCAACAAACAATTTCCC-AGTTCTAGAACCAATTTCAACTCCACGA
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCCCAATTTC-AGAGCCAATTTCAACTTCACGA
*
440052 CGGAGGATATTGGACTC
129 CGAAGGATATTGGACTC
440069 GGAACAATAC
Statistics
Matches: 428, Mismatches: 29, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
313 199 0.46
314 42 0.10
315 187 0.44
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (314 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGAGCCAATTTCAACTTCACGACG
AAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAATA
AACATTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACGCA
AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATTT
Found at i:448921 original size:3 final size:3
Alignment explanation
Indices: 448915--449059 Score: 218
Period size: 3 Copynumber: 47.7 Consensus size: 3
448905 TCATTTAAAT
** *
448915 TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
448963 TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
449011 TTA TTA TTA TTA TTA TTTA TTA TTA TTA ATA TTA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
449058 TT
1 TT
449060 TAAATATTAC
Statistics
Matches: 128, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
3 122 0.95
4 6 0.05
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:451237 original size:20 final size:21
Alignment explanation
Indices: 451214--451265 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
451204 AGAAATTAAA
451214 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
451234 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
451256 -ATT-ATTTATT
1 AATTCATTTATT
451266 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:460594 original size:53 final size:53
Alignment explanation
Indices: 460362--460616 Score: 310
Period size: 53 Copynumber: 4.9 Consensus size: 53
460352 GAGAATCTTG
* * *
460362 GCAGAAGCCACAGTAAAGGATGAATGTG-TGTCAAATGTTTTACGCACA-CTGA
1 GCAGAAG-CACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
*
460414 GCAGAAGCTACAGTAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAGC-ACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
*
460468 GCAGAAGCTACA--TAAAGATGAATGTGTTGTCAAA-GTTTTACGAACATCTGA
1 GCAGAAGC-ACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
* * * * * *
460519 ACA-AAAC-CAGGAAAGGATGAATGTGTGGTCAAATATTTTATGAACAT-TGA
1 GCAGAAGCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
*
460569 GCAGAAGTCACAGGAAAAGATGAATGTATTGTCAAATGTTTTACGAAC
1 GCAGAAG-CACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
460617 CAGTGATTAT
Statistics
Matches: 177, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
48 2 0.01
50 27 0.15
51 33 0.19
52 47 0.27
53 52 0.29
54 16 0.09
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (53 bp):
GCAGAAGCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
Found at i:461775 original size:75 final size:76
Alignment explanation
Indices: 461652--462352 Score: 1234
Period size: 75 Copynumber: 9.4 Consensus size: 76
461642 CTATTTCCCA
461652 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
461716 AAGCCTT-GGGT
65 AAGCCTTCGGGT
461727 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
461791 AGCCTTCGGGT
66 AGCCTTCGGGT
*
461802 CATCTGTAAATCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
461867 ATCC-TCGGGT
66 AGCCTTCGGGT
461877 CATCTGTAAGTCCTTCA--GCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
461939 AGCCTTCGGGT
66 AGCCTTCGGGT
461950 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
462015 AGCCTTCGGGT
66 AGCCTTCGGGT
462026 CATCTGTAAGTCCTTCAGTGCATGATG-TTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
462089 AGCCTTC-GGT
66 AGCCTTCGGGT
462099 CATCTGTAAGTCCTTCAGTG-ATGATGTTTCCAAAAAG-CTTCGGGGAGCTTTTTGATG-TTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC-GGGAGCTTTTTGATGTTTTCA
462161 AAGCCTTCGGGT
65 AAGCCTTCGGGT
*
462173 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
462238 ATCCTTC-GGT
66 AGCCTTCGGGT
462248 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
462313 ATCCTTCGGGT
66 AGCCTTCGGGT
462324 CATCTGT-AGTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
462353 TAAAACATTT
Statistics
Matches: 604, Mismatches: 7, Indels: 30
0.94 0.01 0.05
Matches are distributed among these distances:
72 15 0.02
73 106 0.18
74 97 0.16
75 298 0.49
76 88 0.15
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:462059 original size:223 final size:226
Alignment explanation
Indices: 461652--462352 Score: 1244
Period size: 223 Copynumber: 3.1 Consensus size: 226
461642 CTATTTCCCA
461652 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCAAA
1 CATCTGTAAGTCCTTCAG-GCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTC-AA
461717 AGCCTT-GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTT
64 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
461780 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAATCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
129 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
461845 GGGAGCTTTTTGATGTTTTCAAATCC-TCGGGT
194 GGGAGCTTTTTGATGTTTTCAAATCCTTCGGGT
461877 CATCTGTAAGTCCTTCA-GCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCAAAG
1 CATCTGTAAGTCCTTCAGGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCAAAG
461941 CCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGA
66 CCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGA
462006 TGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATG-TTCC-AAAAGCCTTCGG
131 TGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGG
*
462069 GAGCTTTTTGATGTTTTCAAAGCCTTC-GGT
196 GAGCTTTTTGATGTTTTCAAATCCTTCGGGT
462099 CATCTGTAAGTCCTTCAGTG-ATGATGTTTCCAAAAAG-CTTCGGGGAGCTTTTTGATGTTTCAA
1 CATCTGTAAGTCCTTCAG-GCATGATGTTTCCAAAAAGCCTTC-GGGAGCTTTTTGATGTTTCAA
*
462162 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
64 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
462227 GATGTTTTCAAATCCTTC-GGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
129 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
462291 GGGAGCTTTTTGATGTTTTCAAATCCTTCGGGT
194 GGGAGCTTTTTGATGTTTTCAAATCCTTCGGGT
462324 CATCTGT-AGTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAG-GCATGATGTTT
462353 TAAAACATTT
Statistics
Matches: 461, Mismatches: 5, Indels: 20
0.95 0.01 0.04
Matches are distributed among these distances:
222 97 0.21
223 225 0.49
224 103 0.22
225 36 0.08
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (226 bp):
CATCTGTAAGTCCTTCAGGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTCAAAG
CCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGA
TGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGG
GAGCTTTTTGATGTTTTCAAATCCTTCGGGT
Found at i:462198 original size:298 final size:298
Alignment explanation
Indices: 461652--462351 Score: 1220
Period size: 298 Copynumber: 2.4 Consensus size: 298
461642 CTATTTCCCA
461652 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
461716 AAGCCTT-GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
65 AAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATG-TTCCAAAAAGCCTTCGGGAGCTTTT
461780 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAATCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
129 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAATCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
* *
461845 GGGAGCTTTTTGATGTTTTCAAATCCTCGGGTCATCTGTAAGTCCTTCAGCATGATGTTTCCAAA
194 GGGAGCTTTTTGATGTTTTCAAAGCCTCGGGTCATCTGTAAGCCCTTCAGCATGATGTTTCCAAA
461910 AAGCCTTCGGGAGCTTTTTGATG-TTTCAAAGCCTTCGGGT
259 AAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTC-GGT
461950 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
462015 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTCC-AAAAGCCTTCGGGAGCTTTTTG
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTCCAAAAAGCCTTCGGGAGC-TTTTG
*
462079 ATGTTTTCAAAGCCTTC-GGTCATCTGTAAGTCCTTCAGTG-ATGATGTTTCCAAAAAG-CTTCG
130 ATGTTTTCAAAGCCTTCGGGTCATCTGTAAATCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC-
462141 GGGAGCTTTTTGATG-TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC
194 GGGAGCTTTTTGATGTTTTCAAAGCC-TCGGGTCATCTGTAAGCCCTTCA--GCATGATGTTTCC
*
462205 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCCTTCGGT
256 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGT
462248 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
462313 ATCCTTCGGGTCATCTGT-AGTCCTTCAGTGCATGATGTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTT
462352 TTAAAACATT
Statistics
Matches: 389, Mismatches: 5, Indels: 17
0.95 0.01 0.04
Matches are distributed among these distances:
295 13 0.03
296 54 0.14
297 59 0.15
298 216 0.56
299 47 0.12
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (298 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTCCAAAAAGCCTTCGGGAGCTTTTGA
TGTTTTCAAAGCCTTCGGGTCATCTGTAAATCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGG
GAGCTTTTTGATGTTTTCAAAGCCTCGGGTCATCTGTAAGCCCTTCAGCATGATGTTTCCAAAAA
GCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGT
Found at i:462486 original size:3 final size:3
Alignment explanation
Indices: 462478--462684 Score: 234
Period size: 3 Copynumber: 71.7 Consensus size: 3
462468 TCATTTAAAT
** *
462478 TTA TTA TTA -TA TTA TTA AAA TTA TT- TTA TTA -TA TTA GTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
462522 TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TAA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
462569 TTA TTT TTA -TA TTA TTA TTA ATA TTA TGA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
462616 TTA TT- TTA TCA GTA TTA TTA TTA TTA TT- TT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
462661 TTA TTA GTA GTTA TTA TTA TTA TT
1 TTA TTA TTA -TTA TTA TTA TTA TT
462685 TAATAATAAT
Statistics
Matches: 172, Mismatches: 23, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
2 18 0.10
3 152 0.88
4 2 0.01
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:463391 original size:13 final size:13
Alignment explanation
Indices: 463373--463400 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
463363 ACCACCGTTA
463373 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
463386 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
463399 CG
1 CG
463401 AGTAACGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.32, G:0.61, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:467087 original size:21 final size:22
Alignment explanation
Indices: 467063--467105 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
467053 TAAAATTTGA
467063 ATTTT-TTATAATTAG-TTATTT
1 ATTTTATTA-AATTAGTTTATTT
*
467084 ATTTTATTAAATTTGTTTATTT
1 ATTTTATTAAATTAGTTTATTT
467106 CAAAATTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
ATTTTATTAAATTAGTTTATTT
Found at i:470301 original size:14 final size:14
Alignment explanation
Indices: 470284--470310 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
470274 TGTAACATCA
470284 TCGATGATCACATG
1 TCGATGATCACATG
470298 TCGATGATCACAT
1 TCGATGATCACAT
470311 AATCACTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (14 bp):
TCGATGATCACATG
Found at i:471711 original size:59 final size:59
Alignment explanation
Indices: 471580--471709 Score: 145
Period size: 59 Copynumber: 2.2 Consensus size: 59
471570 TAAATAGTGA
* ** * *
471580 GATGACCATTTTGTAACTTTTAATAGTCGGAAGACTCAACAAAACATCACCTTATAGTC
1 GATGACCATTTTGTAAATTTTAATAGTAAGAAGACTCAACAAAACATCACCCTATAATC
* * * * *
471639 GATAATCATTTTGTAAATTTTAATAGTAAGATGACTCAATAAAGCAAT-ACCCTATAATAC
1 GATGACCATTTTGTAAATTTTAATAGTAAGAAGACTCAACAAAAC-ATCACCCTATAAT-C
471699 GATGACCATTT
1 GATGACCATTT
471710 GTGTGCTTTA
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
59 45 0.79
60 12 0.21
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (59 bp):
GATGACCATTTTGTAAATTTTAATAGTAAGAAGACTCAACAAAACATCACCCTATAATC
Found at i:471963 original size:18 final size:19
Alignment explanation
Indices: 471926--471963 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
471916 TTGTATTTCA
* *
471926 AACTCAAGTCAATGTAACT
1 AACTCAAATCAATATAACT
471945 AACTCAAAT-AATATAACT
1 AACTCAAATCAATATAACT
471963 A
1 A
471964 GAGTTGCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.26
Consensus pattern (19 bp):
AACTCAAATCAATATAACT
Found at i:473037 original size:19 final size:19
Alignment explanation
Indices: 473013--473059 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
473003 TTATTTATTA
473013 AATTATTTCTTTTAATCTC
1 AATTATTTCTTTTAATCTC
473032 AATTATTTCTTTTAATCTC
1 AATTATTTCTTTTAATCTC
473051 AATTATTTC
1 AATTATTTC
473060 AAATTTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTATTTCTTTTAATCTC
Found at i:473142 original size:15 final size:15
Alignment explanation
Indices: 473124--473179 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
473114 ATAAGTTGAA
473124 TTTATAAATTTTATG
1 TTTATAAATTTTATG
473139 TTTAT--A--TTATG
1 TTTATAAATTTTATG
*
473150 TATTATAAATTTTTAAG
1 T-TTATAAA-TTTTATG
473167 TTT-TAAATTTTAT
1 TTTATAAATTTTAT
473180 ATTTTTTCCG
Statistics
Matches: 33, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
11 6 0.18
12 4 0.12
13 1 0.03
14 6 0.18
15 9 0.27
16 2 0.06
17 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (15 bp):
TTTATAAATTTTATG
Found at i:495205 original size:15 final size:15
Alignment explanation
Indices: 495178--495216 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
495168 TGAATAATAT
495178 GACTAAA-TTATAGG
1 GACTAAATTTATAGG
495192 GACTAAATTTATAGG
1 GACTAAATTTATAGG
*
495207 AACTAAATTT
1 GACTAAATTT
495217 GCAACTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (15 bp):
GACTAAATTTATAGG
Found at i:501031 original size:2 final size:2
Alignment explanation
Indices: 501026--501057 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
501016 AGGTCTCTAC
501026 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
501058 AACAGATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:504937 original size:16 final size:17
Alignment explanation
Indices: 504916--504947 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
504906 ATAATAAAAA
504916 AAAATC-GGGTACCCGC
1 AAAATCTGGGTACCCGC
504932 AAAATCTGGGTACCCG
1 AAAATCTGGGTACCCG
504948 ATTACAGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.16
Consensus pattern (17 bp):
AAAATCTGGGTACCCGC
Found at i:505546 original size:2 final size:2
Alignment explanation
Indices: 505539--505570 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
505529 GCATGCATGC
505539 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
505571 CACGTGGGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:526073 original size:21 final size:21
Alignment explanation
Indices: 526033--526074 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
526023 GTAGCAGTAT
*
526033 TGTAGCAGTACATCGGTACAC
1 TGTAGCAGTACATCGATACAC
* *
526054 TGTAGCAGTGCATTGATACAC
1 TGTAGCAGTACATCGATACAC
526075 AATTTATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (21 bp):
TGTAGCAGTACATCGATACAC
Found at i:526181 original size:19 final size:19
Alignment explanation
Indices: 526157--526205 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
526147 TACTGTTCAT
*
526157 TACTATTCATACCGTATAG
1 TACTATTCATACCATATAG
526176 TACTATTCATACCATATAG
1 TACTATTCATACCATATAG
526195 TACTATTCATA
1 TACTATTCATA
526206 AAAACGTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (19 bp):
TACTATTCATACCATATAG
Found at i:527043 original size:23 final size:25
Alignment explanation
Indices: 527008--527057 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
526998 AATCTTATAT
*
527008 GGCACTACGGTGC-AA-TTCTACGC
1 GGCACTACAGTGCAAATTTCTACGC
*
527031 GGCACTTCAGTGCAAATTTCTACGC
1 GGCACTACAGTGCAAATTTCTACGC
527056 GG
1 GG
527058 TCTTTCGGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 11 0.48
24 2 0.09
25 10 0.43
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.24
Consensus pattern (25 bp):
GGCACTACAGTGCAAATTTCTACGC
Found at i:528802 original size:43 final size:44
Alignment explanation
Indices: 528720--528810 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 44
528710 AATTAGCGGT
* *
528720 GTTTGTATCCAAAAACGCCGCTATAGATCTAGACCTTTTGTGGC
1 GTTTGTATCCAAAAACGCCGCTATAGATATAGACCTTTTGTGAC
* * ** *
528764 GTTTGT-TCCAAAAACGCTGCTATATATATCTACTTTTTGTGAC
1 GTTTGTATCCAAAAACGCCGCTATAGATATAGACCTTTTGTGAC
528807 GTTT
1 GTTT
528811 TTTCTTCTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 34 0.85
44 6 0.15
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (44 bp):
GTTTGTATCCAAAAACGCCGCTATAGATATAGACCTTTTGTGAC
Found at i:532123 original size:2 final size:2
Alignment explanation
Indices: 532116--532142 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
532106 ATCAAAATGT
532116 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
532143 CTTAAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:536694 original size:44 final size:44
Alignment explanation
Indices: 536627--536713 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
536617 ATCAATTTTT
*
536627 TAAAAATATATTTATTTACGTGATAGACACCTA-AAACAATCATA
1 TAAAAATACATTTATTTACGTGATAGACACCTAGAAA-AATCATA
* * * *
536671 TAAATATACATTTATTTAGGTGATAGCCATCTAGAAAAATCAT
1 TAAAAATACATTTATTTACGTGATAGACACCTAGAAAAATCAT
536714 GTGAATTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
44 34 0.92
45 3 0.08
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (44 bp):
TAAAAATACATTTATTTACGTGATAGACACCTAGAAAAATCATA
Found at i:537351 original size:23 final size:23
Alignment explanation
Indices: 537325--537369 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
537315 TGAATACATG
* *
537325 TTTAAAATATTATATTTAAATAT
1 TTTAAAAGATAATATTTAAATAT
*
537348 TTTAAAAGGTAATATTTAAATA
1 TTTAAAAGATAATATTTAAATA
537370 ATATTATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
TTTAAAAGATAATATTTAAATAT
Found at i:543854 original size:18 final size:18
Alignment explanation
Indices: 543831--543869 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
543821 TAAGCCACTA
* *
543831 CTCAACTTTCTTCTCGTG
1 CTCAACCTTCTTCTCCTG
543849 CTCAACCTTCTTCTCCTG
1 CTCAACCTTCTTCTCCTG
543867 CTC
1 CTC
543870 CTGTTTCACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.41, G:0.08, T:0.41
Consensus pattern (18 bp):
CTCAACCTTCTTCTCCTG
Found at i:553168 original size:35 final size:35
Alignment explanation
Indices: 553095--553169 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
553085 CGTCACTAAC
**
553095 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
553130 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
553165 AGTAA
1 AGTAA
553170 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:553272 original size:24 final size:24
Alignment explanation
Indices: 553245--553326 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
553235 CATATATCAA
* *
553245 GTCAAGTATCATATCAGAATTCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
553269 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
553293 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
*
553316 GTCAGGTATCA
1 GTCAAGTATCA
553327 TAACATAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.42
24 29 0.58
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:555745 original size:13 final size:13
Alignment explanation
Indices: 555727--555756 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
555717 ACGAGTCAAT
555727 GGTCAACAGGTCG
1 GGTCAACAGGTCG
*
555740 GGTCAACGGGTCG
1 GGTCAACAGGTCG
555753 GGTC
1 GGTC
555757 GGGTAACCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:555758 original size:18 final size:18
Alignment explanation
Indices: 555735--555808 Score: 70
Period size: 17 Copynumber: 4.4 Consensus size: 18
555725 ATGGTCAACA
555735 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
555753 GGTCGGGT-AAC----CG
1 GGTCGGGTCAACGGGTCG
*
555766 GGTCGGGTAAACGGGTCG
1 GGTCGGGTCAACGGGTCG
* * *
555784 AGTC-CGTCAATGGGTCG
1 GGTCGGGTCAACGGGTCG
555801 GGTCGGGT
1 GGTCGGGT
555809 TGTGACCGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
13 10 0.23
14 3 0.07
17 16 0.36
18 15 0.34
ACGTcount: A:0.14, C:0.20, G:0.47, T:0.19
Consensus pattern (18 bp):
GGTCGGGTCAACGGGTCG
Found at i:555767 original size:13 final size:13
Alignment explanation
Indices: 555751--555783 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
555741 GTCAACGGGT
*
555751 CGGGTCGGGTAAC
1 CGGGTCGGGTAAA
555764 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
555777 CGGGTCG
1 CGGGTCG
555784 AGTCCGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:557904 original size:35 final size:35
Alignment explanation
Indices: 557831--557905 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
557821 CGTCACTAAC
**
557831 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
557866 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
557901 AGTAA
1 AGTAA
557906 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:558008 original size:24 final size:24
Alignment explanation
Indices: 557981--558062 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
557971 CATATATCAA
* *
557981 GTCAAGTATCATATCAGAATTCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
558005 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
558029 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
*
558052 GTCAGGTATCA
1 GTCAAGTATCA
558063 TAACATAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.42
24 29 0.58
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:560474 original size:13 final size:13
Alignment explanation
Indices: 560456--560485 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
560446 ACGAGTCAAT
560456 GGTCAACAGGTCG
1 GGTCAACAGGTCG
*
560469 GGTCAACGGGTCG
1 GGTCAACAGGTCG
560482 GGTC
1 GGTC
560486 GGGTAACCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:560487 original size:18 final size:18
Alignment explanation
Indices: 560464--560537 Score: 70
Period size: 17 Copynumber: 4.4 Consensus size: 18
560454 ATGGTCAACA
560464 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
560482 GGTCGGGT-AAC----CG
1 GGTCGGGTCAACGGGTCG
*
560495 GGTCGGGTAAACGGGTCG
1 GGTCGGGTCAACGGGTCG
* * *
560513 AGTC-CGTCAATGGGTCG
1 GGTCGGGTCAACGGGTCG
560530 GGTCGGGT
1 GGTCGGGT
560538 TGTGACCGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
13 10 0.23
14 3 0.07
17 16 0.36
18 15 0.34
ACGTcount: A:0.14, C:0.20, G:0.47, T:0.19
Consensus pattern (18 bp):
GGTCGGGTCAACGGGTCG
Found at i:560496 original size:13 final size:13
Alignment explanation
Indices: 560480--560512 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
560470 GTCAACGGGT
*
560480 CGGGTCGGGTAAC
1 CGGGTCGGGTAAA
560493 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
560506 CGGGTCG
1 CGGGTCG
560513 AGTCCGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:574040 original size:45 final size:45
Alignment explanation
Indices: 573985--574075 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
573975 TATTTAGAAA
573985 TATTTAATTTTAAAATTAATTGCATTAAACATTTATAGATTATGG
1 TATTTAATTTTAAAATTAATTGCATTAAACATTTATAGATTATGG
574030 TATTTAATTTTAAAATTAATTGCATTAAACATTTATAGATTATGG
1 TATTTAATTTTAAAATTAATTGCATTAAACATTTATAGATTATGG
574075 T
1 T
574076 TTAAATTATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (45 bp):
TATTTAATTTTAAAATTAATTGCATTAAACATTTATAGATTATGG
Found at i:574071 original size:24 final size:24
Alignment explanation
Indices: 573999--574071 Score: 80
Period size: 22 Copynumber: 3.2 Consensus size: 24
573989 TAATTTTAAA
573999 ATTAATTGCATTAAACATTTATAG
1 ATTAATTGCATTAAACATTTATAG
* * * * *
574023 ATT-ATGGTATTTAA-TTTTA-AA
1 ATTAATTGCATTAAACATTTATAG
574044 ATTAATTGCATTAAACATTTATAG
1 ATTAATTGCATTAAACATTTATAG
574068 ATTA
1 ATTA
574072 TGGTTTAAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
21 4 0.11
22 12 0.33
23 12 0.33
24 8 0.22
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.45
Consensus pattern (24 bp):
ATTAATTGCATTAAACATTTATAG
Found at i:583506 original size:27 final size:27
Alignment explanation
Indices: 583476--583531 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
583466 AATAATTCAC
583476 GGCTCAAACGGTTCACATGCATGCATT
1 GGCTCAAACGGTTCACATGCATGCATT
*
583503 GGCTCAAATGGTTCACATGCATGCATT
1 GGCTCAAACGGTTCACATGCATGCATT
583530 GG
1 GG
583532 GAGCTGTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (27 bp):
GGCTCAAACGGTTCACATGCATGCATT
Found at i:583689 original size:29 final size:29
Alignment explanation
Indices: 583603--583708 Score: 151
Period size: 29 Copynumber: 3.7 Consensus size: 29
583593 GGAATGGCGT
* * *
583603 CGGGACTACATGGCGACCTAGAGGGTCGT
1 CGGGACTACATGGCGACCTACAAGGTCGC
583632 CGGGACTACATGGCGACCTACAAGGTCGC
1 CGGGACTACATGGCGACCTACAAGGTCGC
583661 CGGGACTACATGGCGACCTACAAGGTCGC
1 CGGGACTACATGGCGACCTACAAGGTCGC
* *
583690 CTAGG-CTGCATGGCGACCT
1 C-GGGACTACATGGCGACCT
583709 CTCTATTCCT
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 69 0.97
30 2 0.03
ACGTcount: A:0.22, C:0.29, G:0.33, T:0.16
Consensus pattern (29 bp):
CGGGACTACATGGCGACCTACAAGGTCGC
Found at i:583772 original size:12 final size:13
Alignment explanation
Indices: 583740--583772 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
583730 TCGTATATGG
583740 CTCGTATGTCACC
1 CTCGTATGTCACC
583753 CTCGTATGTCACC
1 CTCGTATGTCACC
583766 C-CGTATG
1 CTCGTATG
583773 GCTCGTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.15, C:0.36, G:0.18, T:0.30
Consensus pattern (13 bp):
CTCGTATGTCACC
Found at i:583793 original size:45 final size:46
Alignment explanation
Indices: 583729--583818 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 46
583719 GCATGCTCCC
*
583729 CTCGTATATGGCTCGTATGTCACCCTCGTA-TGTCACCCCGTATGG
1 CTCGTATATGGCTCATATGTCACCCTCGTATTGTCACCCCGTATGG
*
583774 CTCGTTTATGGCTCATATGTCACCCTCGTATTGTCACCCCGTATG
1 CTCGTATATGGCTCATATGTCACCCTCGTATTGTCACCCCGTATG
583819 TCGCCTGGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 28 0.67
46 14 0.33
ACGTcount: A:0.16, C:0.31, G:0.20, T:0.33
Consensus pattern (46 bp):
CTCGTATATGGCTCATATGTCACCCTCGTATTGTCACCCCGTATGG
Found at i:587220 original size:42 final size:42
Alignment explanation
Indices: 587161--587244 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
587151 TTTTGGTATG
*
587161 CTTTAATGGGTAGATATGAACGGGGGCGGGGGAACTAGCACA
1 CTTTAATGGGTAGATATGAACGCGGGCGGGGGAACTAGCACA
* *
587203 CTTTAATGGGTATATATGAACGCGGGCGGGGGGACTAGCACA
1 CTTTAATGGGTAGATATGAACGCGGGCGGGGGAACTAGCACA
587245 AAATATGACG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.27, C:0.15, G:0.37, T:0.20
Consensus pattern (42 bp):
CTTTAATGGGTAGATATGAACGCGGGCGGGGGAACTAGCACA
Found at i:590286 original size:31 final size:31
Alignment explanation
Indices: 590248--590333 Score: 86
Period size: 33 Copynumber: 2.7 Consensus size: 31
590238 CGTGCCATTA
*
590248 TTTATATATATTAACTTTAAAAAAAT-ATGTT
1 TTTATATATATTAACTTTAAAAAAATAAT-AT
***
590279 TTTATATAAATACTTAAC-TTAAATTCATAATAT
1 TTTATAT--ATA-TTAACTTTAAAAAAATAATAT
590312 TTTATATATATTAACTTTAAAA
1 TTTATATATATTAACTTTAAAA
590334 GATATTTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
30 5 0.11
31 15 0.33
33 18 0.40
34 7 0.16
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (31 bp):
TTTATATATATTAACTTTAAAAAAATAATAT
Found at i:593863 original size:15 final size:16
Alignment explanation
Indices: 593840--593879 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
593830 TAATTTTTAA
*
593840 TTTCGAGTTTAAAAAT
1 TTTCAAGTTTAAAAAT
*
593856 TTT-AAGTTTACAAAT
1 TTTCAAGTTTAAAAAT
593871 TTTCAAGTT
1 TTTCAAGTT
593880 GAGTTGAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.47
Consensus pattern (16 bp):
TTTCAAGTTTAAAAAT
Found at i:599108 original size:24 final size:24
Alignment explanation
Indices: 599081--599129 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
599071 ACCTATTGAC
599081 TGAAATATGATAAAATCTTATTTT
1 TGAAATATGATAAAATCTTATTTT
599105 TGAAATATGATAAAATCTTATTTT
1 TGAAATATGATAAAATCTTATTTT
599129 T
1 T
599130 ACGTTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (24 bp):
TGAAATATGATAAAATCTTATTTT
Found at i:613961 original size:19 final size:19
Alignment explanation
Indices: 613937--613973 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
613927 CATGTGGTTA
613937 GTTGTTTTGATTTTCGTGT
1 GTTGTTTTGATTTTCGTGT
*
613956 GTTGTTTTGGTTTTCGTG
1 GTTGTTTTGATTTTCGTG
613974 AATGCACTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.05, G:0.30, T:0.62
Consensus pattern (19 bp):
GTTGTTTTGATTTTCGTGT
Found at i:614268 original size:20 final size:20
Alignment explanation
Indices: 614232--614283 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
614222 TGGATAAGCG
*
614232 TATAAAA-TTTAGGAGAACT
1 TATAAAATTTTCGGAGAACT
614251 TATAAAATTTTCGGAGAACT
1 TATAAAATTTTCGGAGAACT
614271 TATAAAATTTTCG
1 TATAAAATTTTCG
614284 AGGAACATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 7 0.23
20 24 0.77
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (20 bp):
TATAAAATTTTCGGAGAACT
Found at i:614289 original size:20 final size:20
Alignment explanation
Indices: 614232--614289 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
614222 TGGATAAGCG
**
614232 TATAAAATTTAGGA-GAACT
1 TATAAAATTTTCGAGGAACT
614251 TATAAAATTTTCG-GAGAACT
1 TATAAAATTTTCGAG-GAACT
614271 TATAAAATTTTCGAGGAAC
1 TATAAAATTTTCGAGGAAC
614290 ATGTTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 11 0.32
20 22 0.65
21 1 0.03
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.33
Consensus pattern (20 bp):
TATAAAATTTTCGAGGAACT
Found at i:620676 original size:20 final size:20
Alignment explanation
Indices: 620653--620704 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
620643 AACGCGATCC
620653 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
620673 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
620693 CCAAAATCGCAA
1 CCAGAATCGCAA
620705 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:620785 original size:20 final size:20
Alignment explanation
Indices: 620760--620953 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
620750 GATTTTCCAT
* *
620760 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
620780 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
620800 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
620820 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
620840 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
620860 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
620880 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
620900 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
620921 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
620941 AATCGCAACGCGA
1 AATCGCAACGCGA
620954 TATTTAAAGT
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:620805 original size:40 final size:39
Alignment explanation
Indices: 620756--620953 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
620746 TTGCGATTTT
* ** *
620756 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
620794 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
620835 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
620875 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
620914 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
620954 TATTTAAAGT
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:620843 original size:60 final size:60
Alignment explanation
Indices: 620760--620952 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
620750 GATTTTCCAT
* ** * *
620760 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
620820 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
620880 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
620941 AATCGCAACGCG
1 AATCGCAACGCG
620953 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:621343 original size:33 final size:33
Alignment explanation
Indices: 621304--621374 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
621294 TTCACTTAGA
*
621304 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
621337 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
621370 TTTCA
1 TTTCA
621375 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:621531 original size:19 final size:19
Alignment explanation
Indices: 621507--621554 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
621497 GCAACGAGAG
621507 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
621526 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
621545 AATCGCAACG
1 AATCGCAACG
621555 AGAGAATCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:621558 original size:52 final size:53
Alignment explanation
Indices: 621466--621584 Score: 177
Period size: 52 Copynumber: 2.3 Consensus size: 53
621456 GCAACGAGAT
***
621466 AAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGAGAGAATCGCAACGCG
*
621519 AAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
621571 AAACCAAAATCGCA
1 AAATGAAAATCGCA
621585 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
52 41 0.68
53 19 0.32
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.10
Consensus pattern (53 bp):
AAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:621602 original size:19 final size:19
Alignment explanation
Indices: 621580--621677 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
621570 GAAACCAAAA
*
621580 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
621599 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
621613 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
621632 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
621646 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
621665 TCGCGTTGCGATT
1 TCGCGTTGCGATT
621678 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:621621 original size:14 final size:14
Alignment explanation
Indices: 621602--621691 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
621592 TTTCATTTCG
621602 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
621616 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
621635 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
621649 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
621666 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
621682 CGTTGCGATT
1 CGTTGCGATT
621692 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:621627 original size:33 final size:33
Alignment explanation
Indices: 621585--621699 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
621575 CAAAATCGCA
621585 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
621618 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
621651 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
621684 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
621700 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:623621 original size:185 final size:184
Alignment explanation
Indices: 623390--623860 Score: 906
Period size: 185 Copynumber: 2.6 Consensus size: 184
623380 TAGATTGCTT
* *
623390 AGTAAATTTATTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
623455 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
623520 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTG-TTTGTCTTTTGGTTGAA
623575 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
623640 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
623705 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTGTCTTTTGGTTGAA
623759 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
623824 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
623861 ATCCATTCAA
Statistics
Matches: 283, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
184 119 0.42
185 164 0.58
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (184 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTGTCTTTTGGTTGAA
Found at i:623704 original size:93 final size:93
Alignment explanation
Indices: 623390--623860 Score: 894
Period size: 93 Copynumber: 5.1 Consensus size: 93
623380 TAGATTGCTT
* *
623390 AGTAAATTTATTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
623455 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
623483 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
623547 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
623575 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
623640 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
623668 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
623732 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
623759 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
623824 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
623852 AGTAAATTT
1 AGTAAATTT
623861 ATCCATTCAA
Statistics
Matches: 371, Mismatches: 4, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
91 79 0.21
92 115 0.31
93 177 0.48
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:623944 original size:19 final size:19
Alignment explanation
Indices: 623904--624032 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
623894 TAGTTTACTT
* *
623904 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
623924 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
623943 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
623962 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
623976 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
623995 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
624009 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
624028 TCGCA
1 TCGCA
624033 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:623983 original size:33 final size:32
Alignment explanation
Indices: 623940--624032 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
623930 CGCGAAACCA
**
623940 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
623972 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
624005 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
624033 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:624030 original size:52 final size:52
Alignment explanation
Indices: 623904--624032 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
623894 TAGTTTACTT
**
623904 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
623956 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
624009 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
624033 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:624064 original size:14 final size:14
Alignment explanation
Indices: 624045--624104 Score: 66
Period size: 14 Copynumber: 3.9 Consensus size: 14
624035 GCGATTTTCA
624045 TTTCGTTGCGATTC
1 TTTCGTTGCGATTC
624059 TTTCGTTGCGATTTTC
1 TTTCGTTGCGA--TTC
624075 ATTTCGCATTGCGATTC
1 -TTTCG--TTGCGATTC
*
624092 TGTCGTTGCGATT
1 TTTCGTTGCGATT
624105 TTCATTTCGC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 19 0.47
16 7 0.17
17 8 0.20
19 6 0.15
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.48
Consensus pattern (14 bp):
TTTCGTTGCGATTC
Found at i:624088 original size:19 final size:18
Alignment explanation
Indices: 624028--624143 Score: 99
Period size: 17 Copynumber: 6.8 Consensus size: 18
624018 GAAACCAAAA
624028 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGATTTTCATT
624047 TCG-TTGCGA--TTC-TT
1 TCGCTTGCGATTTTCATT
624061 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
*
624078 TCGCATTGCGA--TTC-TG
1 TCGC-TTGCGATTTTCATT
624094 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
**
624111 TCGCGTTGCGA-TTTGGTT
1 TCGC-TTGCGATTTTCATT
624129 TCGCGTTGCGATTTT
1 TCGC-TTGCGATTTT
624144 AAGTTCGTGT
Statistics
Matches: 82, Mismatches: 4, Indels: 22
0.76 0.04 0.20
Matches are distributed among these distances:
14 17 0.21
15 3 0.04
16 10 0.12
17 18 0.22
18 16 0.20
19 18 0.22
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.47
Consensus pattern (18 bp):
TCGCTTGCGATTTTCATT
Done.